There is an increasing chorus of US voices among the policy cognoscenti and Congress threatening to stop over 1 billion in US aid to Egypt or to make it dependent upon some politicized certification of Egypt’s democratic bona fides. This course risks undermining the foundations of a core relationship at the very moment when the promise of building a new and reinvigorated partnership is on the horizon. However good it may feel, being right about what the State Department has described as Egypt’s “persecution” of US employees of the International Republican Institute, National Democratic Institute and Freedom House for assisting local civil society groups is not as useful as being smart. The emotive issues highlighted by their conflict with the Egyptian government cannot be permitted to become the centerpiece of bilateral relations. Doing so plays into the hands of counter-revolution, creates the impression that US-Egyptian relations are simply a test of wills, and feeds Egyptian suspicions that the West is using “democracy” as a cynical tool to short-circuit the revolution.

Washington has a choice. It can play the part reserved for it in this sordid drama, or take a very deep breath and keep its eye firmly fixed on its interest in partnership with Egypt as it moves, in fits and starts, towards a better future.

The revolution in Egypt is first and foremost a social upheaval—demanding that rulers respect and honor the dignity of every citizen. The revolt and its imagery are essentially tied to domestic issues. Palestine for example, has not been an important motivator of revolutionary discontent, certainly not as much as it was in the aftermath of the Arab defeat (Nakba) in 1948. Similarly, it is not opposition to US support for and celebration of Egypt’s autocrats — Anwar Sadat and Hosni Mubarak — over recent decades that has brought Egyptians into the streets and polling places.

This is as it should be. But the growing dispute between Washington and Cairo over the treatment of US and European-supported NGOs – unfolding on the margins of the Egyptian revolution — risks strengthening the worst instincts of the still-uncertain Egyptian upheaval and US policy towards one of its closest allies in the region, pushing each down a road of confrontation and dislocation that will serve neither Egypt nor the US national interest.

The dispute between Washington and Cairo over the former’s financial support for the work of foreign and domestic Egyptian organizations promoting democracy in Egypt predates the revolution. The Mubarak regime was understandably opposed in principle to the work of such organizations, and Washington was on the whole solicitous of its opposition.

Mubarak’s ouster and the widespread popular mobilization that precipitated it created a new context for the dispute. Washington and other donors see themselves doing God’s work, instructing willing and now empowered Egyptians in the tools of democracy. As in all things however, the Egyptian government, and particularly the “deep state” headed by the ruling SCAF, viewed the revolution in an entirely different and more complex manner. Throughout 2011, Washington insisted on continuing and even expanding its efforts in this field, notwithstanding official Egypt’s continuing objection.

Like Egyptians themselves, the Obama administration saw an opportunity to push the generals in the direction of freedom and democracy. Washington’s effort however, is insignificant in the broad context of Egypt’s revolution. The social and political forces mobilized for revolutionary change have little need of Washington’s assistance or time to learn the lessons imparted by its well-meaning but overmatched foreign instructors.

In purely political terms, those elements in Egypt most interested in Washington’s helping hand have proved least able to win public support in the polling booths. Revolutions unleash all kinds of sentiments, good and bad. In Egypt, the serial errors of the SCAF, the lingering power of the ancien regime and growing public frustration with the uncertain fruits of revolution have soured the atmosphere and created an explosive context for efforts of the kind that Washington-supported NGO’s promote. What was once a relatively unimportant sideshow now risks moving to center stage, thanks to the mutually reinforcing missteps of all parties.

The Obama administration and Congress view its support for the activities of NDI, Freedom House and IRI as transparent, self-evidently beneficial and benevolent. The view that Egypt should be “punished” for stifling these programs by withholding or cutting military aid is a popular one.

Most Egyptians have a different view. The SCAF retain Mubarak’s distain for foreign interests playing the public square. The state and its legal institutions follow rules and laws that continue to reflect the hostility of the ancien regime towards such activities. The public at large, where the collective memory of foreign demands for special treatment and the long history of malevolent foreign interference in Egypt’s destiny is ever-present, is wary of the outsiders’ “hidden hand” in growing instability and unrest. Counter-revolutionary elements are anxious to exploit these sentiments for their own purposes – to weaken the SCAF, to push someone other than themselves into the bulls eye, to create a convenient scapegoat for all that is wrong in Egypt today. Explaining these realities, however, does not excuse them, neither in Cairo or Washington.

The United States has a real and lasting interest in empowering Egyptian civil society. As the Arab Spring unfolds, the challenge for all parties is to embrace change as it moves societies away from autocracy, regimes of emergency rule, and the crushing of civil society and towards democracy and creation of national political and governing institutions that derive power from their citizens. Undersecretary of State Bill Burns made this point during a recent visit to Cairo.

For their part, Egyptians of all stripes want to maintain good relations with Washington. One leader of the Muslim Brotherhood, whose party won a parliamentary majority in recent elections notes that, “the democratic transition in Egypt is hanging in the balance […] We strongly advise the Americans and the Europeans to support Egypt during this critical period as compensation for the many years they supported a brutal dictatorship.”

Issandr El Amrani is a Cairo-based writer and consultant. His reporting and commentary on the Middle East and North Africa has appeared in The Economist, London Review of Books, Financial Times, The National, The Guardian, Time and other publications. He also publishes one of the longest-running blog in the region, www.arabist.net.